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ToxSci Advance Access originally published online on April 17, 2007
Toxicological Sciences 2007 99(1):26-34; doi:10.1093/toxsci/kfm090
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Published by Oxford University Press 2007.

Toward a Checklist for Exchange and Interpretation of Data from a Toxicology Study

Jennifer M. Fostel*,1, Lyle Burgoon{dagger}, Craig Zwickl{ddagger}, Peter Lord§, J. Christopher Corton, Pierre R. Bushel|, Michael Cunningham||, Liju Fan|||, Stephen W. Edwards, Susan Hester, James Stevens{ddagger}, Weida Tong#, Michael Waters**, ChiHae Yang{dagger}{dagger} and Raymond Tennant||

* NIEHS, LMIT ITSS Contract, Research Triangle Park, North Carolina 27709-2233 {dagger} Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 {ddagger} Lilly Research Laboratory, Greenfield, Indiana 46140 § Johnson and Johnson PRD, Raritan, New Jersey 08869 National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711 | NIEHS, Research Triangle Park, North Carolina 27709-2233 || National Toxicology Program, Research Triangle Park, North Carolina 27709 ||| Ontology Workshop, LLC, Columbia, Maryland 21045-9998 # National Center for Toxicological Research, Jefferson, Arkansas 72079 ** Integrated Life Sciences, Research Triangle Park, North Carolina 27709 {dagger}{dagger} Leadscope, Columbus, Ohio 43212

1 To whom correspondence should be addressed at NIEHS, MD F1-05, PO Box 12233, 111 Alexander Drive, Research Triangle Park, NC, 27709-2233. E-mail: fostel{at}niehs.nih.gov.

Received February 13, 2007; accepted April 3, 2007


  Abstract

Data from toxicology and toxicogenomics studies are valuable, and can be combined for meta-analysis using public data repositories such as Chemical Effects in Biological Systems Knowledgebase, ArrayExpress, and Gene Expression Omnibus. In order to fully utilize the data for secondary analysis, it is necessary to have a description of the study and good annotation of the accompanying data. This study annotation permits sophisticated cross-study comparison and analysis, and allows data from comparable subjects to be identified and fully understood. The Minimal Information About a Microarray Experiment Standard was proposed to permit deposition and sharing of microarray data. We propose the first step toward an analogous standard for a toxicogenomics/toxicology study, by describing a checklist of information that best practices would suggest be included with the study data. When the information in this checklist is deposited together with the study data, the checklist information helps the public explore the study data in context of time, or identify data from similarly treated subjects, and also explore/identify potential sources of experimental variability. The proposed checklist summarizes useful information to include when sharing study data for publication, deposition into a database, or electronic exchange with collaborators. It is not a description of how to carry out an experiment, but a definition of how to describe an experiment. It is anticipated that once a toxicology checklist is accepted and put into use, then toxicology databases can be configured to require and output these fields, making it straightforward to annotate data for interpretation by others.

Key Words: Toxicogenomics; MIAME; Data integration; Database.

This manuscript has been reviewed and approved for publication by the Environmental Protection Agency but does not necessarily reflect the views of the Agency. Mention of trade names or commercial products does not constitute endorsement or recommendations for use.


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